Research workbench
High resolution crystal structure of argos bound to the EGF domain of spitz
Analyse High resolution crystal structure of argos bound to the EGF domain of spitz in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C9A
- Type
- protein
- Length
- 511 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein giant-lens; Protein spitz
- UniProt
- Q00805, Q01083
- Ligands
- BR
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein giant-lens | protein | 208 | 1% helix, 47% strand | Q00805 |
| B | Protein giant-lens | protein | 207 | 3% helix, 48% strand | Q00805 |
| C, D | Protein spitz | protein | 48 | 13% helix, 35% strand | Q01083 |
Ligands and binding sites
- BR · Bromide ion · ion · 18 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.81 | 0.90 | 49 | empty |
| 2 | 429 | 0.75 | 0.84 | 62 | BR |
| 3 | 128 | 0.48 | 0.79 | 22 | empty |
| 4 | 121 | 0.47 | 0.79 | 21 | empty |
| 5 | 155 | 0.44 | 0.75 | 21 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1414 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1333 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 540 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 433 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide (disulfide).
Compared structures
- 3C9A · High Resolution Crystal Structure of Argos bound to the EGF domain of Spitz · the same entry in another collection · chain A against A, TM-score 1.00
- Q00805 · AlphaFold monomer V2.0 prediction for protein giant-lens (Q00805) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q01083 · AlphaFold monomer V2.0 prediction for protein spitz (Q01083) · a predicted model of the same protein · chain C against A, TM-score 0.95
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q00805
- Every structure of UniProt Q01083
- Elsewhere: RCSB PDB 3C9A · PDBe 3C9A · UniProt Q00805 · UniProt Q01083
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